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- EMDB-51365: Cryo-EM structure of human SLC45A4 in lipid nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-51365
TitleCryo-EM structure of human SLC45A4 in lipid nanodiscs
Map data
Sample
  • Organelle or cellular component: Human SLC45A4
    • Protein or peptide: Solute carrier family 45 member 4
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CHOLESTEROL
  • Ligand: water
KeywordsTransporter / SLC / MFS / Polyamine / Spermidine / TRANSPORT PROTEIN
Function / homologysucrose:proton symporter activity / sucrose transport / Major facilitator superfamily / Major Facilitator Superfamily / MFS transporter superfamily / membrane / Solute carrier family 45 member 4
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsMarkusson S / Newstead S
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust215519/Z/19/Z United Kingdom
Wellcome Trust219531/Z/19/Z United Kingdom
CitationJournal: J Struct Biol / Year: 2020
Title: WITHDRAWN: SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time.
Authors: Joseph Caesar / Cyril F Reboul / Chiara Machello / Simon Kiesewetter / Molly L Tang / Justin C Deme / Steven Johnson / Dominika Elmlund / Susan M Lea / Hans Elmlund /
History
DepositionAug 16, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51365.png

Downloads & links

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Map

FileDownload / File: emd_51365.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 199.68 Å		0.83 Å/pix.
x 240 pix.
= 199.68 Å		0.83 Å/pix.
x 240 pix.
= 199.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2149022 - 1.9190196
Average (Standard dev.)0.00045701145 (±0.047814626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51365_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51365_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51365_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human SLC45A4

EntireName: Human SLC45A4
Components
  • Organelle or cellular component: Human SLC45A4
    • Protein or peptide: Solute carrier family 45 member 4
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: Human SLC45A4

SupramoleculeName: Human SLC45A4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 45 member 4

MacromoleculeName: Solute carrier family 45 member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.833883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKMAPQNADP ESMQVQELSV PLPDPQKAGG AEAENCETIS EGSIDRIPMR LWVMHGAVMF GREFCYAMET ALVTPILLQI GLPEQYYSL TWFLSPILGL IFTPLIGSAS DRCTLSWGRR RPFILALCVG VLFGVALFLN GSAIGLALGD VPNRQPIGIV L TVLGVVVL ...String:
MKMAPQNADP ESMQVQELSV PLPDPQKAGG AEAENCETIS EGSIDRIPMR LWVMHGAVMF GREFCYAMET ALVTPILLQI GLPEQYYSL TWFLSPILGL IFTPLIGSAS DRCTLSWGRR RPFILALCVG VLFGVALFLN GSAIGLALGD VPNRQPIGIV L TVLGVVVL DFSADATEGP IRAYLLDVVD SEEQDMALNI HAFSAGLGGA IGYVLGGLDW TQTFLGSWFR TQNQVLFFFA AI IFTVSVA LHLFSIDEEQ YSPQQERSAE EPGALDGGEP HGVPAFPDEV QSEHELALDY PDVDIMRSKS DSALHVPDTA LDL EPELLF LHDIEPSIFH DASYPATPRS TSQELAKTKL PRLATFLKEA AKEDETLLDN HLNEAKVPNG SGSPTKDALG GYTR VDTKP SATSSSMRRR RHAFRRQASS TFSYYGKLGS HCYRYRRANA VVLIKPSRSM SDLYDMQKRQ RQHRHRNQSG ATTSS GDTE SEEGEGETTV RLLWLSMLKM PRELMRLCLC HLLTWFSVIA EAVFYTDFMG QVIFEGDPKA PSNSTAWQAY NAGVKM GCW GLVIYAATGA ICSALLQKYL DNYDLSVRVI YVLGTLGFSV GTAVMAMFPN VYVAMVTIST MGIVSMSISY CPYALLG QY HDIKQYIHHS PGNSKRGFGI DCAILSCQVY ISQILVASAL GGVVDAVGTV RVIPMVASVG SFLGFLTATF LVIYPNVS E EAKEEQKGLS SPLAGEGRAG GNSEKPTVLK LTRKEGLQGP VETESVVLGL NDIFEAQKIE WHEVEGENLY F

UniProtKB: Solute carrier family 45 member 4

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Macromolecule #2: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 2 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 12 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsHuman SLC45A4 reconstituted in MSP1D1 lipid nanodiscs

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 20184 / Average exposure time: 2.5 sec. / Average electron dose: 39.71 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20196090
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 227752
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 200000 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9ghz:
Cryo-EM structure of human SLC45A4 in lipid nanodiscs

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